Hi Nate,

        I do not create any tables manually.  I simply create the database and
setup users and roles.  I do the following:

initdb ­D /local/postgresql/data
pg_ctl ­D /local/postgresql/data ­I /local/postgresql/pgsql.log start
createdb galaxy_1


Sudo su - postgres
pgsql galaxy_1
CREATE USER galaxy
CREATE USER galaxyftp
ALTER ROLE galaxyftp PASSWORD 'dbpassword'
GRANT SELECT ON galaxy_user TO galaxyftp (Note: this fails prior to
launching galaxy server for the first time)

I start galaxy and run 'sh manage_db.sh upgrade'.

0 -> 1... 
done
1 -> 2... 
done
2 -> 3... 
done
3 -> 4... 
done
4 -> 5... 
done
5 -> 6... 
========================================
This migration script changes certain values in the
history_dataset_association.extension
column, specifically 'qual' is chaged to be 'qual454'.
========================================
/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev_
r6498-py2.6.egg/sqlalchemy/sql/compiler.py:336: SAWarning: The SQLAlchemy
psycopg2 dialect now automatically escapes '%' in text() expressions to
'%%'.
  BIND_PARAMS.sub(do_bindparam, self.post_process_text(textclause.text))
done
6 -> 7... 
========================================
This migration script creates the new history_user_share_association
table, and adds
a new boolean type column to the history table.  This provides support for
sharing
histories in the same way that workflows are shared.
========================================
done
7 -> 8... 
========================================
This migration script adds the following new tables for supporting Galaxy
forms:
1) form_definition_current
2) form_definition
3) form_values
4) request_type
5) request
6) sample
7) sample_state
8) sample_event
========================================
done
8 -> 9... 
========================================
This migration script adds a new column to 2 tables:
1) a new boolean type column named 'submitted' to the 'request' table
2) a new string type column named 'bar_code' to the 'sample' table
========================================
done
9 -> 10... 
========================================
This migration script adds the
history_dataset_association_display_at_authorization table, which
allows 'private' datasets to be displayed at external sites without making
them public.

If using mysql, this script will display the following error, which is
corrected in the next migration
script: history_dataset_association_display_at_authorization table failed:
 (OperationalError)
(1059, 'Identifier name
'ix_history_dataset_association_display_at_authorization_update_time'
is too long.
========================================
done
10 -> 11... 
========================================
This script fixes a problem introduced in the previous migration script (
9->10 ).  MySQL
has a name length limit and thus the index
'ix_hdadaa_history_dataset_association_id' has
to be manually created.
========================================
done
11 -> 12... 
========================================
This script adds a new user_address table that is currently only used with
sample requests, where
a user can select from a list of his addresses to associate with the
request.  This script also
drops the request.submitted column which was boolean and replaces it with
a request.state column
which is a string, allowing for more flexibility with request states.
========================================
0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
request_type table failed: (ProgrammingError) column "deleted" of relation
"request_type" already exists
 '\nALTER TABLE "request_type"  ADD deleted BOOLEAN' {}
0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
request_type table failed: (ProgrammingError) column "deleted" of relation
"request_type" already exists
 '\nALTER TABLE "request_type"  ADD deleted BOOLEAN' {}
done
12 -> 13... 
========================================
This migration script eliminates all of the tables that were used for the
1st version of the
library templates where template fields and contents were each stored as a
separate table row
in various library item tables.  All of these tables are dropped in this
script, eliminating all
existing template data.  A total of 14 existing tables are dropped.

We're now basing library templates on Galaxy forms, so field contents are
stored as a jsonified
list in the form_values table.  This script introduces the following 3 new
association tables:
1) library_info_association
2) library_folder_info_association
3) library_dataset_dataset_info_association

If using mysql, this script will throw an (OperationalError) exception due
to a long index name
on the library_dataset_dataset_info_association table, which is OK because
the script creates
an index with a shortened name.
========================================
done
13 -> 14... 

Migration script to add support for "Pages".
  1) Creates Page and PageRevision tables
  2) Adds username column to User table

done
14 -> 15... 

This migration script adds the tables necessary to support tagging of
histories,
datasets, and history-dataset associations (user views of datasets).

If using mysql, this script will display the following error, which is
corrected in the next migration script:
history_dataset_association_tag_association table failed:
(OperationalError) (1059, 'Identifier name
'ix_history_dataset_association_tag_association_history_dataset_association
_id'
is too long)
(ProgrammingError) relation "tag" already exists
 '\nCREATE TABLE tag (\n\tid SERIAL NOT NULL, \n\ttype INTEGER,
\n\tparent_id INTEGER, \n\tname VARCHAR(255), \n\tPRIMARY KEY (id), \n\t
FOREIGN KEY(parent_id) REFERENCES tag (id), \n\t UNIQUE (name)\n)\n\n' {}
done
15 -> 16... 

This script fixes a problem introduced in 0015_tagging.py.  MySQL has a
name length limit and thus the index
'ix_hda_ta_history_dataset_association_id'
has to be manually created.
done
16 -> 17... 
========================================
This script adds 3 indexes to table columns: library_folder.name,
library_dataset.name, library_dataset_dataset_association.name.
========================================
0017_library_item_indexes DEBUG 2011-12-14 15:15:15,400 Adding index
'ix_library_folder_name' to library_folder table failed:
(ProgrammingError) relation "ix_library_folder_name" already exists
 'CREATE INDEX ix_library_folder_name ON library_folder (name)' {}
0017_library_item_indexes DEBUG 2011-12-14 15:15:15,400 Adding index
'ix_library_folder_name' to library_folder table failed:
(ProgrammingError) relation "ix_library_folder_name" already exists
 'CREATE INDEX ix_library_folder_name ON library_folder (name)' {}
0017_library_item_indexes DEBUG 2011-12-14 15:15:15,413 Adding index
'ix_library_dataset_name' to library_dataset table failed:
(ProgrammingError) relation "ix_library_dataset_name" already exists
 'CREATE INDEX ix_library_dataset_name ON library_dataset (name)' {}
0017_library_item_indexes DEBUG 2011-12-14 15:15:15,413 Adding index
'ix_library_dataset_name' to library_dataset table failed:
(ProgrammingError) relation "ix_library_dataset_name" already exists
 'CREATE INDEX ix_library_dataset_name ON library_dataset (name)' {}
done
17 -> 18... 

This migration script provides support for (a) ordering tags by recency and
(b) tagging pages. This script deletes all existing tags.
done
18 -> 19... 
========================================
This script creates a request.folder_id column which is a foreign
key to the library_folder table. This also adds a 'type' and 'layout'
column
to the form_definition table.
========================================
0019_request_library_folder DEBUG 2011-12-14 15:15:16,933 Adding column
'type' to form_definition table failed: (ProgrammingError) column "type"
of relation "form_definition" already exists
 '\nALTER TABLE "form_definition"  ADD type VARCHAR(255)' {}
0019_request_library_folder DEBUG 2011-12-14 15:15:16,933 Adding column
'type' to form_definition table failed: (ProgrammingError) column "type"
of relation "form_definition" already exists
 '\nALTER TABLE "form_definition"  ADD type VARCHAR(255)' {}
0019_request_library_folder DEBUG 2011-12-14 15:15:16,934 Adding column
'layout' to form_definition table failed: (ProgrammingError) column
"layout" of relation "form_definition" already exists
 '\nALTER TABLE "form_definition"  ADD layout BYTEA' {}
0019_request_library_folder DEBUG 2011-12-14 15:15:16,934 Adding column
'layout' to form_definition table failed: (ProgrammingError) column
"layout" of relation "form_definition" already exists
 '\nALTER TABLE "form_definition"  ADD layout BYTEA' {}
done
19 -> 20... 

========================================
This script creates a job_to_output_library_dataset table for allowing
library
uploads to run as regular jobs.  To support this, a library_folder_id
column is
added to the job table, and library_folder/output_library_datasets
relations
are added to the Job object.  An index is also added to the dataset.state
column.
========================================
done
20 -> 21... 

This migration script adds a user preferences table to Galaxy.

done
21 -> 22... 

Migration script to add support for storing visualizations.
  1) Creates Visualization and VisualizationRevision tables

done
22 -> 23... 

Migration script to add columns for tracking whether pages are deleted and
publicly accessible.

done
23 -> 24... 

Remove unique constraint from page slugs to allow creating a page with
the same slug as a deleted page.

done
24 -> 25... 
========================================
This script adds a foreign key to the form_values table in the galaxy_user
table
========================================
done
25 -> 26... 

========================================
This script adds tables needed for Galaxy cloud functionality.
========================================
done
26 -> 27... 
========================================
This migration script adds the request_event table and
removes the state field in the request table
========================================
done
27 -> 28... 
========================================
This script adds the filename_override_metadata column to the
JobExternalOutputMetadata table,
 allowing existing metadata files to be written when using external
metadata and a cluster
set up with read-only access to database/files
========================================
done
28 -> 29... 

This migration script adds a user actions table to Galaxy.

done
29 -> 30... 

Migration script to add column for a history slug.

done
30 -> 31... 

Migration script to (a) add and populate necessary columns for doing
community tagging of histories, datasets, and pages and (b) add table for
doing individual and community tagging of workflows.

SQLite does not support 'ALTER TABLE ADD FOREIGN KEY', so this script will
generate error messages when run against SQLite; however, script does
execute successfully against SQLite.

done
31 -> 32... 

Migration script to add slug column for stored workflow.

done
32 -> 33... 

Migration script to add necessary columns for distinguishing between
viewing/importing and publishing histories, workflows, and pages. Script
adds published column to histories and workflows and importable column to
pages.

done
33 -> 34... 

Migration script to create a table for page-user share association.

done
34 -> 35... 

Migration script to (a) create tables for annotating objects and (b)
create tags for workflow steps.

done
35 -> 36... 

Migration script to add a deleted column to the following tables:
library_info_association, library_folder_info_association,
library_dataset_dataset_info_association.

done
36 -> 37... 

This migration script removes the library_id & folder_id fields in the
'request' table and
adds the same to the 'sample' table. This also adds a 'datatx' column to
request_type table 
to store the sequencer login information. Finally, this adds a
'dataset_files' column to
the sample table. 

done
37 -> 38... 

Migration script to add an inheritable column to the following tables:
library_info_association, library_folder_info_association.
Also, in case of sqlite check if the previous migration script deleted the
request table and if so, restore the table.

done
38 -> 39... 

Migration script to add a synopsis column to the library table.

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 63, in <module>
    main( repository=repo, url=db_url )
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0
.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
    ret = command_func(**kwargs)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0
.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
    return _migrate(url, repository, version, upgrade=True, err=err,
**opts)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0
.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate
    schema.runchange(ver, change, changeset.step)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0
.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange
    change.run(self.engine, step)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0
.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run
    func()
  File 
"lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_tabl
e.py", line 20, in upgrade
    c.create( Library_table )
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0
.5.4-py2.6.egg/migrate/changeset/schema.py", line 365, in create
    engine._run_visitor(visitorcallable, self, *args, **kwargs)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1158, in _run_visitor
    visitorcallable(self.dialect, conn, **kwargs).traverse(element)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 89, in traverse
    return traverse(obj, self.__traverse_options__, self._visitor_dict)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 200, in traverse
    return traverse_using(iterate(obj, opts), obj, visitors)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 194, in traverse_using
    meth(target)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate-0
.5.4-py2.6.egg/migrate/changeset/ansisql.py", line 97, in visit_column
    self.execute()
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1812, in execute
    return self.connection.execute(self.buffer.getvalue())
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 888, in _execute_text
    return self.__execute_context(context)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context
    self._cursor_execute(context.cursor, context.statement,
context.parameters[0], context=context)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute
    self._handle_dbapi_exception(e, statement, parameters, cursor, context)
  File 
"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_dev
_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in
_handle_dbapi_exception
    raise exc.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "synopsis" of
relation "library" already exists
 '\nALTER TABLE "library"  ADD synopsis TEXT' {}

Thanks,
Iry





On 1/3/12 11:41 AM, "Nate Coraor" <n...@bx.psu.edu> wrote:

>On Dec 21, 2011, at 2:49 PM, Iry Witham wrote:
>
>> I have installed a new Galaxy server utilizing the November 18,2011
>>distribution on a SLES 11 VM and cannot get it to launch cleanly.  I am
>>running postgreSQL v. 8.3.9 to create my database.  Once the database is
>>created and running I launch my Galaxy server and within moments all of
>>the PID fail except for the reports_webapp.pid.  When I tail the logs I
>>find the following:
>> 
>> tail reports_webapp.log -
>> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,179 Enabling
>>'httpexceptions' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,194 Enabling
>>'recursive' middleware
>> 
>>/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/Paste-1.6-py2.6.egg
>>/paste/exceptions/serial_number_generator.py:11: DeprecationWarning: the
>>md5 module is deprecated; use hashlib instead
>>   import md5
>> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,272 Enabling
>>'error' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling
>>'trans logger' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,277 Enabling
>>'config' middleware
>> galaxy.webapps.reports.buildapp DEBUG 2011-12-21 14:20:54,294 Enabling
>>'x-forwarded-host' middleware
>> Starting server in PID 20411.
>> serving on 0.0.0.0:9001 view at http://127.0.0.1:9001
>> 
>> tail web0.log - 
>> galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,793 psycopg2 egg
>>successfully loaded for postgres dialect
>> Traceback (most recent call last):
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp
>>.py", line 82, in app_factory
>>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py",
>>line 39, in __init__
>>     create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
>>).get( '__file__', None ), self.config.database_engine_options )
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/model/migrat
>>e/check.py", line 105, in create_or_verify_database
>>     % ( db_schema.version, migrate_repository.versions.latest,
>>config_arg ) )
>> Exception: Your database has version '38' but this code expects version
>>'85'.  Please backup your database and then migrate the schema by
>>running 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade'.
>> Removing PID file web0.pid
>> 
>> tail runner0.log -
>> galaxy.model.migrate.check DEBUG 2011-12-21 14:20:54,789 psycopg2 egg
>>successfully loaded for postgres dialect
>> Traceback (most recent call last):
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/web/buildapp
>>.py", line 82, in app_factory
>>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/app.py",
>>line 39, in __init__
>>     create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
>>).get( '__file__', None ), self.config.database_engine_options )
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/lib/galaxy/model/migrat
>>e/check.py", line 105, in create_or_verify_database
>>     % ( db_schema.version, migrate_repository.versions.latest,
>>config_arg ) )
>> Exception: Your database has version '38' but this code expects version
>>'85'.  Please backup your database and then migrate the schema by
>>running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
>> Removing PID file runner0.pid
>> 
>> 
>> sh manage_db.sh upgrade -
>> 
>> 38 -> 39... 
>> 
>> Migration script to add a synopsis column to the library table.
>> 
>> Traceback (most recent call last):
>>   File "./scripts/manage_db.py", line 63, in <module>
>>     main( repository=repo, url=db_url )
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate
>>-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
>>     ret = command_func(**kwargs)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate
>>-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
>>     return _migrate(url, repository, version, upgrade=True, err=err,
>>**opts)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate
>>-0.5.4-py2.6.egg/migrate/versioning/api.py", line 349, in _migrate
>>     schema.runchange(ver, change, changeset.step)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate
>>-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange
>>     change.run(self.engine, step)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate
>>-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 101, in run
>>     func()
>>   File 
>>"lib/galaxy/model/migrate/versions/0039_add_synopsis_column_to_library_ta
>>ble.py", line 20, in upgrade
>>     c.create( Library_table )
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate
>>-0.5.4-py2.6.egg/migrate/changeset/schema.py", line 365, in create
>>     engine._run_visitor(visitorcallable, self, *args, **kwargs)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1158, in _run_visitor
>>     visitorcallable(self.dialect, conn, **kwargs).traverse(element)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 89, in traverse
>>     return traverse(obj, self.__traverse_options__, self._visitor_dict)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 200, in traverse
>>     return traverse_using(iterate(obj, opts), obj, visitors)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/sql/visitors.py", line 194, in
>>traverse_using
>>     meth(target)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/sqlalchemy_migrate
>>-0.5.4-py2.6.egg/migrate/changeset/ansisql.py", line 97, in visit_column
>>     self.execute()
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1812, in execute
>>     return self.connection.execute(self.buffer.getvalue())
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
>>     return Connection.executors[c](self, object, multiparams, params)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 888, in _execute_text
>>     return self.__execute_context(context)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in
>>__execute_context
>>     self._cursor_execute(context.cursor, context.statement,
>>context.parameters[0], context=context)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in
>>_cursor_execute
>>     self._handle_dbapi_exception(e, statement, parameters, cursor,
>>context)
>>   File 
>>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>ev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in
>>_handle_dbapi_exception
>>     raise exc.DBAPIError.instance(statement, parameters, e,
>>connection_invalidated=is_disconnect)
>> sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "synopsis"
>>of relation "library" already exists
>>  '\nALTER TABLE "library"  ADD synopsis TEXT' {}
>> 
>> I have dropped the database multiple times and recreated it and
>>intentionally left out steps when creating DB users and roles and the
>>manage_db.sh fails at different spots.  However, I cannot get past 38 ->
>>39.  Any suggestions?
>
>Hi Iry,
>
>Can you clarify whether you are manually creating any tables?  You only
>need to create the database itself, Galaxy handles all of the tables.
>
>If you're not creating any tables, what is the output of the very first
>run of Galaxy on an empty database?
>
>--nate
>
>> 
>> Thanks,
>> 
>> IRy
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Description: default.xml

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